Here are my few suggestions. Some of them have already been mentioned before, of course.
1 - There should be possible to organize training camps and friendly tournaments;
2 - There should be a way to tell players why they should come to your team;
3 - There should be a way to tell your players why they should stay in your team, when they want to move to a bigger club - for example, you don´t want to go to Real Madrid because this is the first time after decades we are pushing for continental qualification;
4 - There should be possible to give specific orders to players: dive in the area; hunt down an oposition striker, drible a lot, etc.;
5 - There should be possible to shout orders during a game, like: full atack, focus on right flank, cover left flank, etc; - those orders would have an imediate impact, but: the more you use, the less efective they are; the smaller the pitch, or the greater the attendance, the less efective they are; and, if players don´t speak your language, the less efective they are;
6 - There should be possible to complain about a referee after a game, directly to the FA;
7 - There should be possible to complain about a referee during a game, to put him under pressure - the more it is used, the less efective it is; of course, this can result in manager warnings, bans, and sent offs;
8 - There should be possible to learn new languages;
9 - Players could have traits, like the mercenary one that has been mentioned;
10 - There should be a better media system, in respect to news and press confereces, but I have no idea how this could be done - it would be nice to see, though, some real life problems, like players scandals, and players contact to the media, talking about other players, managers and transfers;
11 - Injuries definetely have to be tweakened;
12 - Sometimes, in very tense games, involving rivalries and finals, there should be general fighting in the pitch - I mean, whole messes involving both squads;
13 - There should be a way, as mentioned, to get coaches reports and comparisons from every position the player can play.